ragout 基因组拼接

ragout 可以将denovo 组装的片段基因组 拼接成一整条长基因组

conda 可以直接下载  https://github.com/fenderglass/Ragout

自己下载要依赖的东西太多，等着conda就行。

输入 一个自己写的file a.rcp;把 references 路径和scaffolds路径放进去 .references = reference .target = scaffolds reference.fasta = references/reference.fasta scaffolds.fasta = MP171004FG.fasta

运行ragout

ragout a.rcp  --outdir aa --refine  --overwrite

如果基因组过小 可能会出现 如下情况。可能是因为block size 太大了 所以可以修改下rcp文件

$ ragout a.rcp  --outdir aa --refine  --overwrite
[10:21:10] INFO: Starting Ragout v2.3
[10:21:10] INFO: Running withs synteny block sizes '[5000, 500, 100]'
[10:21:10] INFO: Running Sibelia with block size 5000
[10:21:11] INFO: Running Sibelia with block size 500
[10:21:13] INFO: Running Sibelia with block size 100
[10:21:14] INFO: Inferring phylogeny from synteny blocks data
[10:21:14] INFO: Reading aa/sibelia-workdir/100/blocks_coords.txt
[10:21:14] INFO: "reference" synteny blocks coverage: 95.77%
[10:21:14] INFO: "scaffolds" synteny blocks coverage: 84.07%
[10:21:14] INFO: Inferred tree: ('reference' : 0.5, 'scaffolds' : 0.5)
[10:21:14] INFO: 'reference' is chosen as a naming reference
[10:21:14] INFO: Processing permutation files
[10:21:14] INFO: Reading aa/sibelia-workdir/5000/blocks_coords.txt
[10:21:14] ERROR: An error occured while running Ragout:
[10:21:14] ERROR: Permutations file is empty

.references = reference
.target = scaffolds
reference.fasta = references/reference.fasta 
scaffolds.fasta = MP171004FG.fasta
.blocks = 200,300,500,1000